How to render depth or surface Normal maps that properly reflect details of 3D shapes while respecting the nature of materials (transparency/glass)?
Yes, if you make the transparent surfaces completely transparent they will not affect the normal and depth passes.

One way to accomplish this with your existing materials is by replacing the output with the "Alpha BSDF" Transparency node when the "Mix Color/Alpha" node is less than 1.



If you are doing this on many objects you may want to look into using node groups and python to automate things.



Also, you may want to add an edge split modifier to get rid of some of those artifacts near sharp edges.